Query psy2116
Match_columns 102
No_of_seqs 127 out of 458
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 16:29:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2116.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2116hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03238 probable histone acet 100.0 2.4E-34 5.2E-39 228.6 6.2 79 24-102 5-83 (290)
2 KOG2747|consensus 100.0 5.3E-33 1.1E-37 228.2 5.7 77 26-102 117-193 (396)
3 PLN00104 MYST -like histone ac 100.0 1E-32 2.2E-37 229.5 5.7 76 27-102 158-233 (450)
4 PTZ00064 histone acetyltransfe 100.0 2E-32 4.4E-37 230.4 5.9 76 27-102 240-315 (552)
5 PLN03239 histone acetyltransfe 100.0 8.1E-32 1.8E-36 218.6 5.8 76 27-102 62-144 (351)
6 COG5027 SAS2 Histone acetyltra 99.9 4.4E-26 9.5E-31 185.9 3.8 68 35-102 126-193 (395)
7 PF00096 zf-C2H2: Zinc finger, 96.9 0.00092 2E-08 33.6 2.1 22 68-89 1-22 (23)
8 PF13894 zf-C2H2_4: C2H2-type 96.3 0.0035 7.5E-08 30.8 2.1 22 68-89 1-22 (24)
9 PF13912 zf-C2H2_6: C2H2-type 95.3 0.016 3.5E-07 30.0 2.1 23 67-89 1-23 (27)
10 PF12171 zf-C2H2_jaz: Zinc-fin 93.8 0.02 4.4E-07 30.1 0.3 21 68-88 2-22 (27)
11 PHA02768 hypothetical protein; 93.6 0.046 1E-06 34.4 1.6 25 67-91 5-29 (55)
12 PF12874 zf-met: Zinc-finger o 93.2 0.1 2.2E-06 26.4 2.3 21 68-88 1-21 (25)
13 smart00355 ZnF_C2H2 zinc finge 92.1 0.099 2.2E-06 25.4 1.4 21 68-88 1-21 (26)
14 PF13913 zf-C2HC_2: zinc-finge 92.0 0.11 2.4E-06 27.4 1.5 24 67-91 2-25 (25)
15 smart00451 ZnF_U1 U1-like zinc 89.9 0.27 5.9E-06 26.4 1.9 22 67-88 3-24 (35)
16 PF13909 zf-H2C2_5: C2H2-type 88.3 0.38 8.3E-06 24.2 1.6 21 68-89 1-21 (24)
17 PHA00616 hypothetical protein 84.8 0.55 1.2E-05 28.3 1.2 23 68-90 2-24 (44)
18 PF12756 zf-C2H2_2: C2H2 type 78.4 1.9 4.1E-05 27.1 2.1 26 66-91 49-74 (100)
19 PHA00732 hypothetical protein 69.6 2.9 6.3E-05 27.5 1.4 21 68-88 2-22 (79)
20 COG5112 UFD2 U1-like Zn-finger 67.0 4.8 0.0001 29.0 2.1 33 56-89 45-77 (126)
21 PF05605 zf-Di19: Drought indu 66.7 4.3 9.3E-05 24.3 1.6 22 67-89 2-23 (54)
22 KOG2462|consensus 63.7 4.2 9E-05 33.1 1.5 26 64-89 212-237 (279)
23 COG4049 Uncharacterized protei 63.1 4.4 9.4E-05 26.2 1.2 28 64-91 14-41 (65)
24 PHA00733 hypothetical protein 62.5 5.7 0.00012 28.1 1.9 24 65-88 71-94 (128)
25 PF02892 zf-BED: BED zinc fing 60.8 5.9 0.00013 22.4 1.4 28 63-90 12-44 (45)
26 smart00614 ZnF_BED BED zinc fi 60.5 6.5 0.00014 23.2 1.6 27 66-92 17-49 (50)
27 PF06220 zf-U1: U1 zinc finger 60.2 6.2 0.00014 22.6 1.4 20 68-87 4-25 (38)
28 KOG3993|consensus 56.3 6.8 0.00015 34.0 1.6 30 63-92 352-381 (500)
29 PF13465 zf-H2C2_2: Zinc-finge 54.1 6.4 0.00014 20.4 0.7 16 64-79 11-26 (26)
30 KOG3576|consensus 47.8 11 0.00024 30.1 1.4 25 64-88 114-138 (267)
31 KOG3576|consensus 47.1 7.8 0.00017 31.0 0.5 26 66-91 144-169 (267)
32 PF07967 zf-C3HC: C3HC zinc fi 46.1 18 0.0004 25.2 2.2 37 65-101 41-101 (133)
33 PHA00733 hypothetical protein 43.6 16 0.00036 25.7 1.7 25 65-89 97-121 (128)
34 smart00548 IRO Motif in Iroquo 39.3 15 0.00033 19.9 0.7 12 5-16 3-14 (26)
35 KOG3623|consensus 37.7 14 0.00029 34.4 0.6 25 64-88 891-915 (1007)
36 smart00734 ZnF_Rad18 Rad18-lik 32.9 32 0.0007 18.0 1.4 21 69-90 3-23 (26)
37 PLN03086 PRLI-interacting fact 32.7 33 0.00071 30.4 2.1 31 65-95 502-542 (567)
38 COG5236 Uncharacterized conser 31.0 27 0.0006 30.0 1.3 21 68-88 221-241 (493)
39 PF07623 PEGSRP: Protein of un 28.6 28 0.00061 19.0 0.7 8 92-99 4-11 (27)
40 PRK10167 hypothetical protein; 28.2 6.1 0.00013 29.6 -2.7 60 3-62 82-162 (169)
41 PF11672 DUF3268: Protein of u 28.1 35 0.00075 23.7 1.3 22 57-78 21-42 (102)
42 PF12013 DUF3505: Protein of u 27.4 50 0.0011 22.1 1.9 24 66-89 79-106 (109)
43 PF09237 GAGA: GAGA factor; I 27.3 59 0.0013 20.5 2.1 27 63-89 20-46 (54)
44 COG5189 SFP1 Putative transcri 26.5 15 0.00032 31.2 -1.0 28 62-89 393-420 (423)
45 KOG3623|consensus 25.7 25 0.00055 32.7 0.3 26 63-88 946-971 (1007)
46 KOG3608|consensus 25.4 59 0.0013 28.0 2.4 37 62-98 347-384 (467)
47 KOG2462|consensus 25.1 37 0.00079 27.7 1.1 30 64-93 240-269 (279)
48 PF08209 Sgf11: Sgf11 (transcr 24.7 25 0.00053 19.8 -0.0 26 66-92 3-28 (33)
49 PF03048 Herpes_UL92: UL92 fam 24.6 36 0.00079 26.2 0.9 18 60-77 13-30 (192)
50 KOG3408|consensus 23.8 59 0.0013 23.7 1.8 24 66-89 56-79 (129)
51 KOG1074|consensus 23.4 50 0.0011 31.0 1.7 32 65-96 905-936 (958)
52 KOG3993|consensus 22.7 42 0.00091 29.3 1.0 29 64-92 455-483 (500)
53 KOG3608|consensus 22.0 38 0.00081 29.2 0.6 24 65-88 235-258 (467)
54 PF07150 DUF1390: Protein of u 21.8 23 0.0005 28.0 -0.6 27 65-92 5-32 (229)
55 PF04780 DUF629: Protein of un 20.9 66 0.0014 27.9 1.9 24 66-89 56-79 (466)
56 COG0056 AtpA F0F1-type ATP syn 20.8 44 0.00096 29.3 0.8 20 82-101 262-286 (504)
57 KOG0402|consensus 20.4 27 0.00059 24.1 -0.5 16 65-80 34-49 (92)
No 1
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=100.00 E-value=2.4e-34 Score=228.62 Aligned_cols=79 Identities=44% Similarity=0.966 Sum_probs=76.9
Q ss_pred cChHHhhhcCCCCCCCCEEEecCeEEeeccCCCCccccCCCCceeeehhhhcccCCHHHHHHHHhhCCCCCCCCccccC
Q psy2116 24 FSQEAELKTLPNTRGTKYLQMGKYEMEVWYQSPYPDDYARLPKLYLCEFCLKYMKTKTILFRHANKCVWKHPPGEEVYR 102 (102)
Q Consensus 24 ~~~e~e~~~~~~~kNI~~V~fG~y~i~tWY~SPYP~e~~~~~~LYICE~ClkY~~s~~~l~rH~~kC~~r~PPG~eIYR 102 (102)
..+++||++++++|||++|+||+|+|+|||+||||+++.+.++||||||||+||+++.+|.+|+.+|+++||||+||||
T Consensus 5 ~~~~~~~ee~t~~kni~~i~~G~y~i~~WY~SPyP~e~~~~~~lyiCe~Clky~~~~~~l~~H~~~C~~r~PPG~eIYr 83 (290)
T PLN03238 5 AELEREHEETTKVKNIEMIELGKYEMDTWYYSPYPEPYASCTKLYICEYCLKYMRKKKSLLRHLAKCDIRQPPGGGIYG 83 (290)
T ss_pred hHHHhcchhhhcCCCcCEEEECCeeeecCccCCCChHHcCCCeEEEcCCCcchhCCHHHHHHHHHhCCCCCCCcCEeEe
Confidence 4578999999999999999999999999999999999999999999999999999999999999999999999999997
No 2
>KOG2747|consensus
Probab=99.97 E-value=5.3e-33 Score=228.24 Aligned_cols=77 Identities=52% Similarity=1.126 Sum_probs=74.3
Q ss_pred hHHhhhcCCCCCCCCEEEecCeEEeeccCCCCccccCCCCceeeehhhhcccCCHHHHHHHHhhCCCCCCCCccccC
Q psy2116 26 QEAELKTLPNTRGTKYLQMGKYEMEVWYQSPYPDDYARLPKLYLCEFCLKYMKTKTILFRHANKCVWKHPPGEEVYR 102 (102)
Q Consensus 26 ~e~e~~~~~~~kNI~~V~fG~y~i~tWY~SPYP~e~~~~~~LYICE~ClkY~~s~~~l~rH~~kC~~r~PPG~eIYR 102 (102)
.+.++.+.++++||+.|+||+|+|+|||+||||+|++++++||||||||+||++++.|++|+.+|.++|||||||||
T Consensus 117 ~~~~~~~~~~~r~i~~i~~G~yei~~WY~SPyP~e~~~~~~lYiCEfCLkY~~s~~~l~rH~~kC~~rhPPG~EIYR 193 (396)
T KOG2747|consen 117 LEQEHEEVEKVRNIEKIEFGRYEIKTWYFSPYPEEYAKLDKLYICEFCLKYMKSRTSLQRHLKKCKLRHPPGNEIYR 193 (396)
T ss_pred hhccccccceecccceEEEcceeeeeeecCCCchhhccCCeEEEehHHHhHhchHHHHHHHHHhcCCCCCCcceeee
Confidence 45777788999999999999999999999999999999999999999999999999999999999999999999998
No 3
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=99.97 E-value=1e-32 Score=229.47 Aligned_cols=76 Identities=46% Similarity=1.022 Sum_probs=73.8
Q ss_pred HHhhhcCCCCCCCCEEEecCeEEeeccCCCCccccCCCCceeeehhhhcccCCHHHHHHHHhhCCCCCCCCccccC
Q psy2116 27 EAELKTLPNTRGTKYLQMGKYEMEVWYQSPYPDDYARLPKLYLCEFCLKYMKTKTILFRHANKCVWKHPPGEEVYR 102 (102)
Q Consensus 27 e~e~~~~~~~kNI~~V~fG~y~i~tWY~SPYP~e~~~~~~LYICE~ClkY~~s~~~l~rH~~kC~~r~PPG~eIYR 102 (102)
.+|++++|++|||++|+||+|+|+||||||||+|+...++||||||||+||+++.+|.+|+.+|+++||||+||||
T Consensus 158 l~~~ee~tk~kni~~i~~G~y~i~~WY~SPyP~e~~~~~~lyiCe~Cl~y~~~~~~~~~H~~~C~~~~PPG~eIYr 233 (450)
T PLN00104 158 LREHEEFTKVKNIATIELGRYEIDTWYFSPFPPEYNDCSKLYFCEFCLKFMKRKEQLQRHMKKCDLKHPPGDEIYR 233 (450)
T ss_pred ccccccccccCccCEEEECCeEeeeeecCCCChHHcCCCeEEEchhhhhhhcCHHHHHHHHhcCCCCCCCcCeEEE
Confidence 3578999999999999999999999999999999999999999999999999999999999999999999999997
No 4
>PTZ00064 histone acetyltransferase; Provisional
Probab=99.97 E-value=2e-32 Score=230.43 Aligned_cols=76 Identities=34% Similarity=0.837 Sum_probs=73.9
Q ss_pred HHhhhcCCCCCCCCEEEecCeEEeeccCCCCccccCCCCceeeehhhhcccCCHHHHHHHHhhCCCCCCCCccccC
Q psy2116 27 EAELKTLPNTRGTKYLQMGKYEMEVWYQSPYPDDYARLPKLYLCEFCLKYMKTKTILFRHANKCVWKHPPGEEVYR 102 (102)
Q Consensus 27 e~e~~~~~~~kNI~~V~fG~y~i~tWY~SPYP~e~~~~~~LYICE~ClkY~~s~~~l~rH~~kC~~r~PPG~eIYR 102 (102)
.+||+++|++|||++|+||+|+|+||||||||+++..+++||||||||+||+++.+|.+|+.+|.++||||+||||
T Consensus 240 ~kehee~tkvkNI~~I~~G~yei~TWYfSPYP~Ey~~~d~LYICEfCLkY~~s~~~l~rH~~~C~~rhPPG~EIYR 315 (552)
T PTZ00064 240 ILDHEETTRLRTIGRVRIGKFILDTWYFSPLPDEYQNVDTLHFCEYCLDFFCFEDELIRHLSRCQLRHPPGNEIYR 315 (552)
T ss_pred hhcchhhhcCCCcCeEEECCeEecCCcCCCCChhhcCCCeEEEccchhhhhCCHHHHHHHHhcCCCCCCCCCeEEE
Confidence 3678899999999999999999999999999999999999999999999999999999999999999999999997
No 5
>PLN03239 histone acetyltransferase; Provisional
Probab=99.97 E-value=8.1e-32 Score=218.58 Aligned_cols=76 Identities=34% Similarity=0.808 Sum_probs=71.5
Q ss_pred HHhhhcCCCCCCCCEEEecCeEEeeccCCCCccccCC----CCceeeehhhhcccCCHHHHHHHHhh---CCCCCCCCcc
Q psy2116 27 EAELKTLPNTRGTKYLQMGKYEMEVWYQSPYPDDYAR----LPKLYLCEFCLKYMKTKTILFRHANK---CVWKHPPGEE 99 (102)
Q Consensus 27 e~e~~~~~~~kNI~~V~fG~y~i~tWY~SPYP~e~~~----~~~LYICE~ClkY~~s~~~l~rH~~k---C~~r~PPG~e 99 (102)
.+|+++++++|||++|+||+|+|+||||||||+++.+ +++||||||||+||+++.+|.+|+.+ |..+||||+|
T Consensus 62 ~~~~~e~t~~rNI~~I~~G~y~i~tWYfSPyP~e~~~~~~~~~~lYiCE~Clky~~~~~~l~~H~~~~~~c~~~~PPG~e 141 (351)
T PLN03239 62 LKEHEEVTKVKNVAFLELGPYQMDTWYFSPLPKELFKAGGFIDVLYVCEFSFGFFARKSELLRFQAKELPKERRHPPGNE 141 (351)
T ss_pred hhhhHHHhcCCCCCEEEECCeeecCCCCCCCcHHHhcccccCceEEEeccchhhhcCHHHHHHHHHhhccccCcCCCCCe
Confidence 3578899999999999999999999999999999964 79999999999999999999999987 7889999999
Q ss_pred ccC
Q psy2116 100 VYR 102 (102)
Q Consensus 100 IYR 102 (102)
|||
T Consensus 142 IYR 144 (351)
T PLN03239 142 IYR 144 (351)
T ss_pred EEE
Confidence 997
No 6
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=99.92 E-value=4.4e-26 Score=185.95 Aligned_cols=68 Identities=47% Similarity=1.121 Sum_probs=66.7
Q ss_pred CCCCCCEEEecCeEEeeccCCCCccccCCCCceeeehhhhcccCCHHHHHHHHhhCCCCCCCCccccC
Q psy2116 35 NTRGTKYLQMGKYEMEVWYQSPYPDDYARLPKLYLCEFCLKYMKTKTILFRHANKCVWKHPPGEEVYR 102 (102)
Q Consensus 35 ~~kNI~~V~fG~y~i~tWY~SPYP~e~~~~~~LYICE~ClkY~~s~~~l~rH~~kC~~r~PPG~eIYR 102 (102)
.++||..|.+|+|++++||+||||.++++.+.+|||||||+||.+...|.||+++|+++|||||||||
T Consensus 126 ~v~~i~~i~~~~y~iepwyfSpyp~~~s~~d~vyICefClkY~~s~~~~~rH~~kC~~~~pPG~eiYr 193 (395)
T COG5027 126 RVKNINEIKLGNYEIEPWYFSPYPEEFSDLDIVYICEFCLKYYGSQTSLVRHRKKCSLQHPPGNEIYR 193 (395)
T ss_pred hhccchhheecccccccccccCcchhhcccceEEEhhhhHHHhcchhHHHHHHhcCcCcCCCCceeee
Confidence 57899999999999999999999999999999999999999999999999999999999999999998
No 7
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.86 E-value=0.00092 Score=33.62 Aligned_cols=22 Identities=36% Similarity=0.680 Sum_probs=20.9
Q ss_pred eeehhhhcccCCHHHHHHHHhh
Q psy2116 68 YLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 68 YICE~ClkY~~s~~~l~rH~~k 89 (102)
|.|+.|-+-|+++..|.+|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 7899999999999999999975
No 8
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.34 E-value=0.0035 Score=30.79 Aligned_cols=22 Identities=27% Similarity=0.602 Sum_probs=18.8
Q ss_pred eeehhhhcccCCHHHHHHHHhh
Q psy2116 68 YLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 68 YICE~ClkY~~s~~~l~rH~~k 89 (102)
|.|+.|.+-|++..+|.+|+..
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 7899999999999999999975
No 9
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=95.28 E-value=0.016 Score=30.00 Aligned_cols=23 Identities=22% Similarity=0.403 Sum_probs=21.1
Q ss_pred eeeehhhhcccCCHHHHHHHHhh
Q psy2116 67 LYLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 67 LYICE~ClkY~~s~~~l~rH~~k 89 (102)
+|.|+.|-+-|.+...|.+|++.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCCccCCccCChhHHHHHhHH
Confidence 58999999999999999999963
No 10
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=93.84 E-value=0.02 Score=30.09 Aligned_cols=21 Identities=29% Similarity=0.743 Sum_probs=19.7
Q ss_pred eeehhhhcccCCHHHHHHHHh
Q psy2116 68 YLCEFCLKYMKTKTILFRHAN 88 (102)
Q Consensus 68 YICE~ClkY~~s~~~l~rH~~ 88 (102)
|.|+.|-+.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 789999999999999999985
No 11
>PHA02768 hypothetical protein; Provisional
Probab=93.57 E-value=0.046 Score=34.42 Aligned_cols=25 Identities=20% Similarity=0.366 Sum_probs=22.5
Q ss_pred eeeehhhhcccCCHHHHHHHHhhCC
Q psy2116 67 LYLCEFCLKYMKTKTILFRHANKCV 91 (102)
Q Consensus 67 LYICE~ClkY~~s~~~l~rH~~kC~ 91 (102)
-|.|+.|.+.|+..+.|.+|+++=.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC
Confidence 4899999999999999999998743
No 12
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.17 E-value=0.1 Score=26.38 Aligned_cols=21 Identities=24% Similarity=0.645 Sum_probs=19.8
Q ss_pred eeehhhhcccCCHHHHHHHHh
Q psy2116 68 YLCEFCLKYMKTKTILFRHAN 88 (102)
Q Consensus 68 YICE~ClkY~~s~~~l~rH~~ 88 (102)
|.|+-|-+-|.+...|..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 689999999999999999985
No 13
>smart00355 ZnF_C2H2 zinc finger.
Probab=92.13 E-value=0.099 Score=25.40 Aligned_cols=21 Identities=38% Similarity=0.616 Sum_probs=19.6
Q ss_pred eeehhhhcccCCHHHHHHHHh
Q psy2116 68 YLCEFCLKYMKTKTILFRHAN 88 (102)
Q Consensus 68 YICE~ClkY~~s~~~l~rH~~ 88 (102)
|.|+.|-+-|.+...+..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 579999999999999999987
No 14
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.97 E-value=0.11 Score=27.37 Aligned_cols=24 Identities=25% Similarity=0.510 Sum_probs=21.2
Q ss_pred eeeehhhhcccCCHHHHHHHHhhCC
Q psy2116 67 LYLCEFCLKYMKTKTILFRHANKCV 91 (102)
Q Consensus 67 LYICE~ClkY~~s~~~l~rH~~kC~ 91 (102)
|-.|..|.+-| ....+.+|++.|.
T Consensus 2 l~~C~~CgR~F-~~~~l~~H~~~C~ 25 (25)
T PF13913_consen 2 LVPCPICGRKF-NPDRLEKHEKICK 25 (25)
T ss_pred CCcCCCCCCEE-CHHHHHHHHHhcC
Confidence 45799999999 8889999999985
No 15
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=89.86 E-value=0.27 Score=26.45 Aligned_cols=22 Identities=14% Similarity=0.360 Sum_probs=20.1
Q ss_pred eeeehhhhcccCCHHHHHHHHh
Q psy2116 67 LYLCEFCLKYMKTKTILFRHAN 88 (102)
Q Consensus 67 LYICE~ClkY~~s~~~l~rH~~ 88 (102)
.|-|+.|-+.|.+...+..|..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4789999999999999999985
No 16
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=88.30 E-value=0.38 Score=24.20 Aligned_cols=21 Identities=38% Similarity=0.787 Sum_probs=15.7
Q ss_pred eeehhhhcccCCHHHHHHHHhh
Q psy2116 68 YLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 68 YICE~ClkY~~s~~~l~rH~~k 89 (102)
|.|+.|- |..++..|.+|++.
T Consensus 1 y~C~~C~-y~t~~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCS-YSTSKSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS--EESHHHHHHHHHH
T ss_pred CCCCCCC-CcCCHHHHHHHHHh
Confidence 6799998 55559999999874
No 17
>PHA00616 hypothetical protein
Probab=84.77 E-value=0.55 Score=28.33 Aligned_cols=23 Identities=22% Similarity=0.394 Sum_probs=21.1
Q ss_pred eeehhhhcccCCHHHHHHHHhhC
Q psy2116 68 YLCEFCLKYMKTKTILFRHANKC 90 (102)
Q Consensus 68 YICE~ClkY~~s~~~l~rH~~kC 90 (102)
|-|..|.+-|..+++|.+|+.+-
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~ 24 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSV 24 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHh
Confidence 78999999999999999999763
No 18
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=78.43 E-value=1.9 Score=27.13 Aligned_cols=26 Identities=19% Similarity=0.491 Sum_probs=22.1
Q ss_pred ceeeehhhhcccCCHHHHHHHHhhCC
Q psy2116 66 KLYLCEFCLKYMKTKTILFRHANKCV 91 (102)
Q Consensus 66 ~LYICE~ClkY~~s~~~l~rH~~kC~ 91 (102)
.-+.|..|.+-|.+...|..|++.-.
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 36999999999999999999998643
No 19
>PHA00732 hypothetical protein
Probab=69.61 E-value=2.9 Score=27.53 Aligned_cols=21 Identities=29% Similarity=0.365 Sum_probs=19.8
Q ss_pred eeehhhhcccCCHHHHHHHHh
Q psy2116 68 YLCEFCLKYMKTKTILFRHAN 88 (102)
Q Consensus 68 YICE~ClkY~~s~~~l~rH~~ 88 (102)
|.|+.|.+-|.+...|.+|++
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhh
Confidence 679999999999999999986
No 20
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=67.00 E-value=4.8 Score=28.99 Aligned_cols=33 Identities=27% Similarity=0.545 Sum_probs=26.6
Q ss_pred CCccccCCCCceeeehhhhcccCCHHHHHHHHhh
Q psy2116 56 PYPDDYARLPKLYLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 56 PYP~e~~~~~~LYICE~ClkY~~s~~~l~rH~~k 89 (102)
||-.++-.+..-|-| -|-+||.+...|..|.+-
T Consensus 45 p~Dp~lPGlGqhYCi-eCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 45 PYDPELPGLGQHYCI-ECARYFITEKALMEHKKG 77 (126)
T ss_pred CCCCCCCCCceeeee-hhHHHHHHHHHHHHHhcc
Confidence 676777777666655 599999999999999864
No 21
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=66.71 E-value=4.3 Score=24.28 Aligned_cols=22 Identities=23% Similarity=0.548 Sum_probs=17.9
Q ss_pred eeeehhhhcccCCHHHHHHHHhh
Q psy2116 67 LYLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 67 LYICE~ClkY~~s~~~l~rH~~k 89 (102)
-|.|.||.+ --+...|..|...
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~ 23 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCED 23 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHh
Confidence 378999999 5667899999754
No 22
>KOG2462|consensus
Probab=63.73 E-value=4.2 Score=33.08 Aligned_cols=26 Identities=23% Similarity=0.346 Sum_probs=23.3
Q ss_pred CCceeeehhhhcccCCHHHHHHHHhh
Q psy2116 64 LPKLYLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 64 ~~~LYICE~ClkY~~s~~~l~rH~~k 89 (102)
-++-|.|..|-|-|.+++.|..|++.
T Consensus 212 GEKPF~C~hC~kAFADRSNLRAHmQT 237 (279)
T KOG2462|consen 212 GEKPFSCPHCGKAFADRSNLRAHMQT 237 (279)
T ss_pred CCCCccCCcccchhcchHHHHHHHHh
Confidence 47889999999999999999999975
No 23
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=63.05 E-value=4.4 Score=26.19 Aligned_cols=28 Identities=21% Similarity=0.345 Sum_probs=24.7
Q ss_pred CCceeeehhhhcccCCHHHHHHHHhhCC
Q psy2116 64 LPKLYLCEFCLKYMKTKTILFRHANKCV 91 (102)
Q Consensus 64 ~~~LYICE~ClkY~~s~~~l~rH~~kC~ 91 (102)
-+.++-|..|.+-|..+.++.||..+--
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 4678999999999999999999998743
No 24
>PHA00733 hypothetical protein
Probab=62.48 E-value=5.7 Score=28.09 Aligned_cols=24 Identities=25% Similarity=0.539 Sum_probs=17.5
Q ss_pred CceeeehhhhcccCCHHHHHHHHh
Q psy2116 65 PKLYLCEFCLKYMKTKTILFRHAN 88 (102)
Q Consensus 65 ~~LYICE~ClkY~~s~~~l~rH~~ 88 (102)
+.-|.|+.|.+-|.+...|.+|+.
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHh
Confidence 445777777777777777777775
No 25
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=60.80 E-value=5.9 Score=22.39 Aligned_cols=28 Identities=32% Similarity=0.402 Sum_probs=18.8
Q ss_pred CCCceeeehhhhcccCCH----HHHHHHH-hhC
Q psy2116 63 RLPKLYLCEFCLKYMKTK----TILFRHA-NKC 90 (102)
Q Consensus 63 ~~~~LYICE~ClkY~~s~----~~l~rH~-~kC 90 (102)
..+..-.|-+|.+-++.. +.|.+|+ .+|
T Consensus 12 ~~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 12 GDKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp GCSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CCcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 456778999999988775 8999999 445
No 26
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=60.45 E-value=6.5 Score=23.17 Aligned_cols=27 Identities=26% Similarity=0.367 Sum_probs=20.9
Q ss_pred ceeeehhhhcccCCH-----HHHHHHHh-hCCC
Q psy2116 66 KLYLCEFCLKYMKTK-----TILFRHAN-KCVW 92 (102)
Q Consensus 66 ~LYICE~ClkY~~s~-----~~l~rH~~-kC~~ 92 (102)
.-=+|.+|.+-++.. +.|.+|+. +|+.
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~~ 49 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHPA 49 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCcC
Confidence 356799998877655 79999999 6764
No 27
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=60.24 E-value=6.2 Score=22.63 Aligned_cols=20 Identities=35% Similarity=0.979 Sum_probs=9.5
Q ss_pred eeehhhhcccC--CHHHHHHHH
Q psy2116 68 YLCEFCLKYMK--TKTILFRHA 87 (102)
Q Consensus 68 YICE~ClkY~~--s~~~l~rH~ 87 (102)
|-||||-.++. +...-..|.
T Consensus 4 yyCdyC~~~~~~d~~~~Rk~H~ 25 (38)
T PF06220_consen 4 YYCDYCKKYLTHDSPSIRKQHE 25 (38)
T ss_dssp -B-TTT--B-S--SHHHHHHHT
T ss_pred eecccccceecCCChHHHHHhh
Confidence 78999999994 334445564
No 28
>KOG3993|consensus
Probab=56.27 E-value=6.8 Score=34.02 Aligned_cols=30 Identities=17% Similarity=0.315 Sum_probs=26.3
Q ss_pred CCCceeeehhhhcccCCHHHHHHHHhhCCC
Q psy2116 63 RLPKLYLCEFCLKYMKTKTILFRHANKCVW 92 (102)
Q Consensus 63 ~~~~LYICE~ClkY~~s~~~l~rH~~kC~~ 92 (102)
..+.+|.|..|+|-|+.+.-|..|+..|..
T Consensus 352 ss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 352 SSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred ccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 346799999999999999999999887764
No 29
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=54.06 E-value=6.4 Score=20.35 Aligned_cols=16 Identities=31% Similarity=0.592 Sum_probs=12.9
Q ss_pred CCceeeehhhhcccCC
Q psy2116 64 LPKLYLCEFCLKYMKT 79 (102)
Q Consensus 64 ~~~LYICE~ClkY~~s 79 (102)
.++.|.|+.|-+-|.+
T Consensus 11 ~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 11 GEKPYKCPYCGKSFSN 26 (26)
T ss_dssp SSSSEEESSSSEEESS
T ss_pred CCCCCCCCCCcCeeCc
Confidence 3577999999998863
No 30
>KOG3576|consensus
Probab=47.78 E-value=11 Score=30.15 Aligned_cols=25 Identities=24% Similarity=0.433 Sum_probs=22.3
Q ss_pred CCceeeehhhhcccCCHHHHHHHHh
Q psy2116 64 LPKLYLCEFCLKYMKTKTILFRHAN 88 (102)
Q Consensus 64 ~~~LYICE~ClkY~~s~~~l~rH~~ 88 (102)
...++.|.-|.|-|.-+..|.||++
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~k 138 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLK 138 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhh
Confidence 3678999999999999999999986
No 31
>KOG3576|consensus
Probab=47.09 E-value=7.8 Score=30.98 Aligned_cols=26 Identities=35% Similarity=0.451 Sum_probs=22.3
Q ss_pred ceeeehhhhcccCCHHHHHHHHhhCC
Q psy2116 66 KLYLCEFCLKYMKTKTILFRHANKCV 91 (102)
Q Consensus 66 ~LYICE~ClkY~~s~~~l~rH~~kC~ 91 (102)
+-|+|.||.|=|....+|.||.+.-+
T Consensus 144 kr~lct~cgkgfndtfdlkrh~rtht 169 (267)
T KOG3576|consen 144 KRHLCTFCGKGFNDTFDLKRHTRTHT 169 (267)
T ss_pred HHHHHhhccCcccchhhhhhhhcccc
Confidence 45899999999999999999987543
No 32
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=46.13 E-value=18 Score=25.23 Aligned_cols=37 Identities=22% Similarity=0.525 Sum_probs=25.1
Q ss_pred CceeeehhhhcccCCH-----------------HHH-----HHHHhhCCCC-CCCC-cccc
Q psy2116 65 PKLYLCEFCLKYMKTK-----------------TIL-----FRHANKCVWK-HPPG-EEVY 101 (102)
Q Consensus 65 ~~LYICE~ClkY~~s~-----------------~~l-----~rH~~kC~~r-~PPG-~eIY 101 (102)
...-.|+.|-+...-+ ..+ ..|...|++| .+-. +.+|
T Consensus 41 ~d~l~C~~C~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~H~~~CpWr~~~cpl~~~~ 101 (133)
T PF07967_consen 41 KDMLKCESCGARLCVKLSDSPPDLDSEVYKKLVEKYSEQLVTGHKESCPWRNNSCPLDSLY 101 (133)
T ss_pred CCEEEeCCCCCEEEEeccccchHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCChhhhh
Confidence 5677899998877655 233 7899999996 3333 4444
No 33
>PHA00733 hypothetical protein
Probab=43.60 E-value=16 Score=25.75 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=22.3
Q ss_pred CceeeehhhhcccCCHHHHHHHHhh
Q psy2116 65 PKLYLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 65 ~~LYICE~ClkY~~s~~~l~rH~~k 89 (102)
...|.|+.|-+-|.....|.+|+.+
T Consensus 97 ~~~~~C~~CgK~F~~~~sL~~H~~~ 121 (128)
T PHA00733 97 EHSKVCPVCGKEFRNTDSTLDHVCK 121 (128)
T ss_pred CcCccCCCCCCccCCHHHHHHHHHH
Confidence 3468999999999999999999975
No 34
>smart00548 IRO Motif in Iroquois-class homeodomain proteins (only). Unknown function.
Probab=39.32 E-value=15 Score=19.95 Aligned_cols=12 Identities=42% Similarity=0.825 Sum_probs=9.5
Q ss_pred cCCCCCcchhhH
Q psy2116 5 SRKPRPWSLINW 16 (102)
Q Consensus 5 ~~~~~~~~~~~~ 16 (102)
..||+=|||-|-
T Consensus 3 ~~KPKIWSLAet 14 (26)
T smart00548 3 AAKPKIWSLADT 14 (26)
T ss_pred CCCCceeeHHHh
Confidence 469999998664
No 35
>KOG3623|consensus
Probab=37.69 E-value=14 Score=34.44 Aligned_cols=25 Identities=28% Similarity=0.533 Sum_probs=22.6
Q ss_pred CCceeeehhhhcccCCHHHHHHHHh
Q psy2116 64 LPKLYLCEFCLKYMKTKTILFRHAN 88 (102)
Q Consensus 64 ~~~LYICE~ClkY~~s~~~l~rH~~ 88 (102)
-+-+|+|+-|-|-|...+.|.||.-
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKY 915 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKY 915 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhh
Confidence 4679999999999999999999983
No 36
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=32.89 E-value=32 Score=18.03 Aligned_cols=21 Identities=19% Similarity=0.751 Sum_probs=17.7
Q ss_pred eehhhhcccCCHHHHHHHHhhC
Q psy2116 69 LCEFCLKYMKTKTILFRHANKC 90 (102)
Q Consensus 69 ICE~ClkY~~s~~~l~rH~~kC 90 (102)
-|.-|.+-+ +.....+|...|
T Consensus 3 ~CPiC~~~v-~~~~in~HLD~C 23 (26)
T smart00734 3 QCPVCFREV-PENLINSHLDSC 23 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHHHh
Confidence 478888888 778999999877
No 37
>PLN03086 PRLI-interacting factor K; Provisional
Probab=32.67 E-value=33 Score=30.41 Aligned_cols=31 Identities=19% Similarity=0.405 Sum_probs=23.2
Q ss_pred CceeeehhhhcccC----------CHHHHHHHHhhCCCCCC
Q psy2116 65 PKLYLCEFCLKYMK----------TKTILFRHANKCVWKHP 95 (102)
Q Consensus 65 ~~LYICE~ClkY~~----------s~~~l~rH~~kC~~r~P 95 (102)
.+++.|+||.+-+. ....|..|...|..++-
T Consensus 502 ~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~ 542 (567)
T PLN03086 502 LRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTA 542 (567)
T ss_pred CCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcce
Confidence 57889999988774 24578899888876643
No 38
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=31.00 E-value=27 Score=29.95 Aligned_cols=21 Identities=38% Similarity=0.657 Sum_probs=19.5
Q ss_pred eeehhhhcccCCHHHHHHHHh
Q psy2116 68 YLCEFCLKYMKTKTILFRHAN 88 (102)
Q Consensus 68 YICE~ClkY~~s~~~l~rH~~ 88 (102)
=.|+||-++|-+..+|.+|++
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR 241 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCR 241 (493)
T ss_pred chhhhccceecChHHHHHHHH
Confidence 479999999999999999986
No 39
>PF07623 PEGSRP: Protein of unknown function (DUF1584); InterPro: IPR011477 This sequence motif is highly conserved in several short hypothetical proteins from Rhodopirellula baltica. It is also associated with IPR011476 from INTERPRO in Q7UJJ9 from SWISSPROT.
Probab=28.65 E-value=28 Score=19.01 Aligned_cols=8 Identities=75% Similarity=1.934 Sum_probs=6.3
Q ss_pred CCCCCCcc
Q psy2116 92 WKHPPGEE 99 (102)
Q Consensus 92 ~r~PPG~e 99 (102)
+|.|||.+
T Consensus 4 ~RkppG~~ 11 (27)
T PF07623_consen 4 WRKPPGEE 11 (27)
T ss_pred cccCCCCC
Confidence 57899975
No 40
>PRK10167 hypothetical protein; Provisional
Probab=28.19 E-value=6.1 Score=29.60 Aligned_cols=60 Identities=15% Similarity=0.060 Sum_probs=38.3
Q ss_pred cccCCCCCcchhhHHHHHhhhcCh-----H-HhhhcC-C-----CCCCCCEEEe---------cCeEEeeccCCCCcccc
Q psy2116 3 ACSRKPRPWSLINWFYFALVLFSQ-----E-AELKTL-P-----NTRGTKYLQM---------GKYEMEVWYQSPYPDDY 61 (102)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~-----e-~e~~~~-~-----~~kNI~~V~f---------G~y~i~tWY~SPYP~e~ 61 (102)
|-+++|.+=+.+|-.+=..+.|+. | +|+.++ . .++-+.=|.+ -.|..+..|.+|||+++
T Consensus 82 al~~~~t~~~~~NvL~Hi~GYFKk~Ls~~EKq~l~~lI~~Yr~g~vpl~vpltlL~h~~~~y~~~YL~~Q~yL~PyP~~L 161 (169)
T PRK10167 82 LLSHPANVRDHTNVLMHVQGYFRPHIDSTERQQLAALIDSYRRGEQPLLAPLMRIKHYMALYPDAWLSGQRYFELWPRVI 161 (169)
T ss_pred HHcCCCCcchhHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHCCcHHHHhCcCCCCCChHH
Confidence 456778888888866655555544 2 133111 1 3444444556 57888999999999976
Q ss_pred C
Q psy2116 62 A 62 (102)
Q Consensus 62 ~ 62 (102)
.
T Consensus 162 ~ 162 (169)
T PRK10167 162 N 162 (169)
T ss_pred c
Confidence 3
No 41
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=28.08 E-value=35 Score=23.74 Aligned_cols=22 Identities=36% Similarity=0.775 Sum_probs=16.4
Q ss_pred CccccCCCCceeeehhhhcccC
Q psy2116 57 YPDDYARLPKLYLCEFCLKYMK 78 (102)
Q Consensus 57 YP~e~~~~~~LYICE~ClkY~~ 78 (102)
||..+..-+-+|||+-|-.|-.
T Consensus 21 Yg~~~~~~~~~y~C~~C~AyVG 42 (102)
T PF11672_consen 21 YGHRYDDGPYLYVCTPCDAYVG 42 (102)
T ss_pred cCccCCCCceeEECCCCCceee
Confidence 5656555677899999988754
No 42
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=27.44 E-value=50 Score=22.06 Aligned_cols=24 Identities=25% Similarity=0.437 Sum_probs=21.9
Q ss_pred ceeee----hhhhcccCCHHHHHHHHhh
Q psy2116 66 KLYLC----EFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 66 ~LYIC----E~ClkY~~s~~~l~rH~~k 89 (102)
.-|.| +.|.-.+.+...|.+|.++
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~ 106 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRK 106 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHH
Confidence 66999 9999999999999999864
No 43
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=27.26 E-value=59 Score=20.46 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=19.0
Q ss_pred CCCceeeehhhhcccCCHHHHHHHHhh
Q psy2116 63 RLPKLYLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 63 ~~~~LYICE~ClkY~~s~~~l~rH~~k 89 (102)
....--.|.-|-.-+.+...|.||+..
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHH
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHH
Confidence 346778999999999999999999963
No 44
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=26.53 E-value=15 Score=31.17 Aligned_cols=28 Identities=32% Similarity=0.375 Sum_probs=23.7
Q ss_pred CCCCceeeehhhhcccCCHHHHHHHHhh
Q psy2116 62 ARLPKLYLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 62 ~~~~~LYICE~ClkY~~s~~~l~rH~~k 89 (102)
.-.++-|.||+|-|-.+....|.-|+..
T Consensus 393 ~~~~KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 393 SAKDKPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred cccCCceeccccchhhccCccceecccc
Confidence 3457999999999999999999888753
No 45
>KOG3623|consensus
Probab=25.67 E-value=25 Score=32.75 Aligned_cols=26 Identities=27% Similarity=0.430 Sum_probs=22.6
Q ss_pred CCCceeeehhhhcccCCHHHHHHHHh
Q psy2116 63 RLPKLYLCEFCLKYMKTKTILFRHAN 88 (102)
Q Consensus 63 ~~~~LYICE~ClkY~~s~~~l~rH~~ 88 (102)
.-++-|-|+-|+|=|++...|.+||.
T Consensus 946 SGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 946 SGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred cCCCcchhhhhhhhcccccchHhhhc
Confidence 34788999999999999999999985
No 46
>KOG3608|consensus
Probab=25.41 E-value=59 Score=28.00 Aligned_cols=37 Identities=27% Similarity=0.558 Sum_probs=31.1
Q ss_pred CCCCceeeehhhhcccCCHHHHHHHHhh-CCCCCCCCc
Q psy2116 62 ARLPKLYLCEFCLKYMKTKTILFRHANK-CVWKHPPGE 98 (102)
Q Consensus 62 ~~~~~LYICE~ClkY~~s~~~l~rH~~k-C~~r~PPG~ 98 (102)
.+.+.+|-|--|-+.|++...|.+|..+ =..+-|-|-
T Consensus 347 g~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsGh 384 (467)
T KOG3608|consen 347 GNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSGH 384 (467)
T ss_pred CCCCCceeeecchhhhccchhHHHHHHHhhcccCCCCC
Confidence 3678999999999999999999999976 445677674
No 47
>KOG2462|consensus
Probab=25.09 E-value=37 Score=27.72 Aligned_cols=30 Identities=27% Similarity=0.294 Sum_probs=26.0
Q ss_pred CCceeeehhhhcccCCHHHHHHHHhhCCCC
Q psy2116 64 LPKLYLCEFCLKYMKTKTILFRHANKCVWK 93 (102)
Q Consensus 64 ~~~LYICE~ClkY~~s~~~l~rH~~kC~~r 93 (102)
..+-|-|..|-|+|.-++-|.+|...+..+
T Consensus 240 ~~K~~qC~~C~KsFsl~SyLnKH~ES~C~~ 269 (279)
T KOG2462|consen 240 DVKKHQCPRCGKSFALKSYLNKHSESACLK 269 (279)
T ss_pred CCccccCcchhhHHHHHHHHHHhhhhcccc
Confidence 357899999999999999999999875543
No 48
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=24.70 E-value=25 Score=19.84 Aligned_cols=26 Identities=19% Similarity=0.345 Sum_probs=19.4
Q ss_pred ceeeehhhhcccCCHHHHHHHHhhCCC
Q psy2116 66 KLYLCEFCLKYMKTKTILFRHANKCVW 92 (102)
Q Consensus 66 ~LYICE~ClkY~~s~~~l~rH~~kC~~ 92 (102)
..+.|.-|.+... ..-+..|..+|--
T Consensus 3 ~~~~C~nC~R~v~-a~RfA~HLekCmg 28 (33)
T PF08209_consen 3 PYVECPNCGRPVA-ASRFAPHLEKCMG 28 (33)
T ss_dssp -EEE-TTTSSEEE-GGGHHHHHHHHTC
T ss_pred CeEECCCCcCCcc-hhhhHHHHHHHHc
Confidence 4688999999765 5678999999854
No 49
>PF03048 Herpes_UL92: UL92 family; InterPro: IPR004289 Members of this family are functionally uncharacterised proteins from herpesviruses. The N terminus of these proteins contain 6 conserved cysteines and histidines that might form a zinc binding domain.
Probab=24.59 E-value=36 Score=26.19 Aligned_cols=18 Identities=28% Similarity=0.866 Sum_probs=14.7
Q ss_pred ccCCCCceeeehhhhccc
Q psy2116 60 DYARLPKLYLCEFCLKYM 77 (102)
Q Consensus 60 e~~~~~~LYICE~ClkY~ 77 (102)
.+.++..+|+|+-|.+|-
T Consensus 13 ~~~~v~~vfvC~~c~~~H 30 (192)
T PF03048_consen 13 SYHQVGNVFVCEKCGRYH 30 (192)
T ss_pred chhcCceEEEeCCCCCEE
Confidence 345689999999999883
No 50
>KOG3408|consensus
Probab=23.82 E-value=59 Score=23.74 Aligned_cols=24 Identities=21% Similarity=0.440 Sum_probs=20.9
Q ss_pred ceeeehhhhcccCCHHHHHHHHhh
Q psy2116 66 KLYLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 66 ~LYICE~ClkY~~s~~~l~rH~~k 89 (102)
-.|-|=.|-+||.+...|+.|.+.
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 357788999999999999999864
No 51
>KOG1074|consensus
Probab=23.36 E-value=50 Score=31.03 Aligned_cols=32 Identities=34% Similarity=0.822 Sum_probs=18.2
Q ss_pred CceeeehhhhcccCCHHHHHHHHhhCCCCCCC
Q psy2116 65 PKLYLCEFCLKYMKTKTILFRHANKCVWKHPP 96 (102)
Q Consensus 65 ~~LYICE~ClkY~~s~~~l~rH~~kC~~r~PP 96 (102)
++-|.|.||-+-|.++..|+-||.+=.|..||
T Consensus 905 ~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~ 936 (958)
T KOG1074|consen 905 PKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPP 936 (958)
T ss_pred CCCccchhhhhhhhhhhhhhhhhccccccCCC
Confidence 44566666666666666666666554444554
No 52
>KOG3993|consensus
Probab=22.72 E-value=42 Score=29.32 Aligned_cols=29 Identities=28% Similarity=0.504 Sum_probs=26.4
Q ss_pred CCceeeehhhhcccCCHHHHHHHHhhCCC
Q psy2116 64 LPKLYLCEFCLKYMKTKTILFRHANKCVW 92 (102)
Q Consensus 64 ~~~LYICE~ClkY~~s~~~l~rH~~kC~~ 92 (102)
....|-|++|..-|-+...|.||..+|-.
T Consensus 455 ~~q~f~~ky~~atfyss~~ltrhin~~Hp 483 (500)
T KOG3993|consen 455 AEQGFTCKYCPATFYSSPGLTRHINKCHP 483 (500)
T ss_pred hhhccccccchHhhhcCcchHhHhhhcCh
Confidence 46789999999999999999999999964
No 53
>KOG3608|consensus
Probab=22.02 E-value=38 Score=29.17 Aligned_cols=24 Identities=25% Similarity=0.533 Sum_probs=20.8
Q ss_pred CceeeehhhhcccCCHHHHHHHHh
Q psy2116 65 PKLYLCEFCLKYMKTKTILFRHAN 88 (102)
Q Consensus 65 ~~LYICE~ClkY~~s~~~l~rH~~ 88 (102)
..-|.|..|+|.|.++..|..|+.
T Consensus 235 ~n~fqC~~C~KrFaTeklL~~Hv~ 258 (467)
T KOG3608|consen 235 TNSFQCAQCFKRFATEKLLKSHVV 258 (467)
T ss_pred CCchHHHHHHHHHhHHHHHHHHHH
Confidence 457899999999999999988885
No 54
>PF07150 DUF1390: Protein of unknown function (DUF1390); InterPro: IPR009820 This entry is represented by Paramecium bursaria Chlorella virus 1, A79R; it is a family of uncharacterised viral proteins.
Probab=21.83 E-value=23 Score=27.96 Aligned_cols=27 Identities=26% Similarity=0.361 Sum_probs=23.5
Q ss_pred CceeeehhhhcccCCHHHHHHHHh-hCCC
Q psy2116 65 PKLYLCEFCLKYMKTKTILFRHAN-KCVW 92 (102)
Q Consensus 65 ~~LYICE~ClkY~~s~~~l~rH~~-kC~~ 92 (102)
-+||+| -|.-.+.+...-.+|.+ +|..
T Consensus 5 ~~lY~C-~CGYkT~~~gnAsKHkKtsC~h 32 (229)
T PF07150_consen 5 ITLYTC-GCGYKTTNKGNASKHKKTSCGH 32 (229)
T ss_pred EEEEEe-cCCceecCCccccccCCCcCCC
Confidence 369999 59999999999999998 6764
No 55
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=20.92 E-value=66 Score=27.90 Aligned_cols=24 Identities=17% Similarity=0.519 Sum_probs=21.8
Q ss_pred ceeeehhhhcccCCHHHHHHHHhh
Q psy2116 66 KLYLCEFCLKYMKTKTILFRHANK 89 (102)
Q Consensus 66 ~LYICE~ClkY~~s~~~l~rH~~k 89 (102)
+=++|.+|-+-|.+..++..|+..
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHH
Confidence 468999999999999999999964
No 56
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=20.82 E-value=44 Score=29.33 Aligned_cols=20 Identities=40% Similarity=0.725 Sum_probs=13.4
Q ss_pred HHHHHHhhC-----CCCCCCCcccc
Q psy2116 82 ILFRHANKC-----VWKHPPGEEVY 101 (102)
Q Consensus 82 ~l~rH~~kC-----~~r~PPG~eIY 101 (102)
+|..|..-+ -+|+|||+|=|
T Consensus 262 DLsKhA~AYReiSLLlrRPPGREAy 286 (504)
T COG0056 262 DLSKHAVAYREISLLLRRPPGREAY 286 (504)
T ss_pred CchHHHHHHHHHHHHhcCCCCccCC
Confidence 455555443 35899999976
No 57
>KOG0402|consensus
Probab=20.42 E-value=27 Score=24.06 Aligned_cols=16 Identities=31% Similarity=0.632 Sum_probs=12.2
Q ss_pred CceeeehhhhcccCCH
Q psy2116 65 PKLYLCEFCLKYMKTK 80 (102)
Q Consensus 65 ~~LYICE~ClkY~~s~ 80 (102)
..-|.|+||.|..-.+
T Consensus 34 haky~CsfCGK~~vKR 49 (92)
T KOG0402|consen 34 HAKYTCSFCGKKTVKR 49 (92)
T ss_pred hhhhhhhhcchhhhhh
Confidence 4579999999876443
Done!